@ejn;
Like 3DGuy said...we need some more information here.
Did you do any post processing?...if so, what?
What is the exif data?

A few points;

1. Long exposures tend to accentuate noise
2. High ISO accentuates noise
3. Bumping up the exposure after the fact (even in RAW) accentuates noise.

Do a quick test...take a 30 sec exposure at the same ISO and Fstop as the one with your ND1000.....EXCEPT leave the lens cap ON!  Do NOT Process the image...take a look at it...is it as noisy as the one with the lens cap off?

In saying all of this....I have routinely shot borealis, noctilucent cloud and nightime lightning images with my old D70 in excess of 30sec at up to ISO 400...NO noise reduction applied in cam.....absolutely NO noise of any kind is visible.

Further, I have friends who have done 20+ minute exposures with both the D200 and D300...they have come out clean!

So...something seems to be amiss here in your situation.....

My only other thought here is that you accidentally ordered the B+W "Swiss Cheese" filter instead of the ND1000......

In youth, we learn....with age, we understand.